[maker-devel] Error running MAKER

Thu Nov 24 19:04:59 MST 2016

A lock failure can become an issue if two separate jobs are running simultaneously. They may both try to process the same contig at the same time (modifying each others files) which will cause one or both to fail. On failure, it should always retry at some later point. So it can usually recover from this. If you see any partial lines in the resulting GFF3, then it did not recover and you need to just rerun whatever contig this happened on.

—Carson

> On Nov 18, 2016, at 12:14 PM, John Cornelius <jcornel3 at asu.edu> wrote:
> 
> Would the lock failure cause problems with the annotation? It looks like Maker is still progressing, just not as quickly as I thought it would be.
> 
> On Thu, Nov 17, 2016 at 9:04 PM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> To use less RAM, try lowering max_dna_len=, setting blast_depth= parameters to 20 pr 30 in maker_bopts.ctl (default is limitless), or when using MPI, starting fewer processes per node (requires manipulation of hostfile or using round robin distribution flag for MPI flavors where it is available).
> 
> The memory issue could be causing the lock failure as well.
> 
> —Carson
> 
> 
> 
>> On Nov 17, 2016, at 7:53 PM, John Cornelius <jcornel3 at asu.edu <mailto:jcornel3 at asu.edu>> wrote:
>> 
>> Ok, so I went and searched one of the output logs for all the lines that say ERROR and I got 44 lines with the following message:
>> 
>> ERROR: Lock broken in runlog
>> 
>> With these lines found at the end:
>> 
>> ERROR: Failed while polishig ESTs
>> ERROR: Chunk failed at level:2, tier_type:3
>> ERROR: Could not query process table: Cannot allocate memory at /packages/maker/2.31.8/bin/../lib/Proc/ProcessTable_simple.pm line 62.
>> 
>> From that last line it looks like the process is running out of RAM would that be right? Thanks.
>> 
>> On Fri, Nov 11, 2016 at 2:59 PM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>> The cause of the error is probably further back in the STDERR. With MPI so many processes are producing status and notes, that you can get several seconds of output after ta failure. If you kept the whole STDERR, I can help you look through it.  searching for “ERROR” all caps is usually where you will see it. Also MAKER keeps a log of progress, so even on failure, you can just restart it and it will pick up the analysis from the last successful step.
>> 
>> —Carson
>> 
>> 
>>> On Nov 10, 2016, at 3:43 PM, John Cornelius <jcornel3 at asu.edu <mailto:jcornel3 at asu.edu>> wrote:
>>> 
>>> Hello, I'm using MAKER to annotate a tetraploid genome and while running it, I encountered the following error:
>>> 
>>> #--------- command -------------#
>>> Widget::exonerate::est2genome:
>>> /packages/exonerate-2.2.0/bin/exonerate  -q /tmp/maker_08Elxf/15/TRINITY_GG_19079_c1670_g1_i1.for.84770203-84771247.15.fasta -t /tmp/maker_08Elxf/15/chr9_10L.84770203-84771247.15.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/maker_08Elxf/15/chr9_10L.84770203-84771247.TRINITY_GG_19079_c1670_g1_i1.e.exonerate
>>> #-------------------------------#
>>> running  est2genome search.
>>> #--------- command -------------#
>>> Widget::exonerate::est2genome:
>>> /packages/exonerate-2.2.0/bin/exonerate  -q /tmp/maker_08Elxf/10/TRINITY_GG_87963_c9694_g10_i12.for.49475083-49475985.10.fasta -t /tmp/maker_08Elxf/10/chr6L.49475083-49475985.10.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/maker_08Elxf/10/chr6L.49475083-49475985.TRINITY_GG_87963_c9694_g10_i12.e.exonerate
>>> #-------------------------------#
>>> 
>>> ===================================================================================
>>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>> =   PID 132376 RUNNING AT pnap-pe7-s03
>>> =   EXIT CODE: 135
>>> =   CLEANING UP REMAINING PROCESSES
>>> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>> ===================================================================================
>>> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Bus error (signal 7)
>>> This typically refers to a problem with your application.
>>> Please see the FAQ page for debugging suggestions
>>> 
>>> The the command I ran was the following:
>>> 
>>> #PBS -l walltime=240:00:00
>>> #PBS -N MAKER
>>> #PBS -l nodes=1:ppn=16
>>> ##PBS -q hmem
>>> #PBS -j oe
>>> #PBS -m abe
>>> #PBS -M jcornelius at tgen.org <mailto:jcornelius at tgen.org>
>>> #PBS -A tgen-205000
>>> #PBS -o /scratch/jcornelius/xenopus_laevis/maker_run
>>> 
>>> # --- load required modules --- #
>>> 
>>> module load maker
>>> 
>>> # --- run maker --- #
>>> 
>>> cd /scratch/jcornelius/xenopus_laevis/maker_run
>>> mpiexec -n 16 maker -base XLNEURO.run1 -fix_nucleotides
>>> 
>>> I'm not sure what could be causing this error and any help would be much appreciated. Thanks.
>>> -- 
>>> John Cornelius
>>> MCB PhD Candidate
>>> Arizona State University
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
>> 
>> 
>> 
>> -- 
>> John Cornelius
>> MCB PhD Candidate
>> Arizona State University
> 
> 
> 
> 
> -- 
> John Cornelius
> MCB PhD Candidate
> Arizona State University

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